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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ), 'gf_id' => 'HOM05D001153', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001153' ), 'data_identifier' => 'HOM05D001153', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001153', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '536', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42630' => 'bna', 'A03p13790' => 'bna', 'A03p44310' => 'bna', 'A04p13690' => 'bna', 'A06p29980' => 'bna', 'A06p33730' => 'bna', 'A07p03380' => 'bna', 'A07p20410' => 'bna', 'A09p11470' => 'bna', 'A10p13070' => 'bna', 'Aa31LG1G18740' => 'aar', 'Aa31LG3G11750' => 'aar', 'Aa31LG4G17030' => 'aar', 'Aa31LG6G12620' => 'aar', 'Aa31sc202G20' => 'aar', 'Aa31sc762G20' => 'aar', 'Actinidia04997' => 'ach', 'Actinidia05952' => 'ach', 'Actinidia06569' => 'ach', 'Actinidia19378' => 'ach', 'Actinidia30392' => 'ach', 'Actinidia35408' => 'ach', 'Actinidia36150' => 'ach', 'Actinidia36783' => 'ach', 'Actinidia37146' => 'ach', 'Ah.04g166620' => 'amhyb', 'Ah.12g059420' => 'amhyb', 'AL3G42050' => 'aly', 'AL3G50630' => 'aly', 'AL5G27860' => 'aly', 'AL7G15480' => 'aly', 'AL7G49100' => 'aly', 'AL8G31420' => 'aly', 'AL8G40350' => 'aly', 'Aqoxy1G04269' => 'aox', 'Aqoxy4G01887' => 'aox', 'Aqoxy5G03609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y3NBD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A5S2D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F2U9KI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P38TYM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USI8UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USIB3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z38NHD' => 'arhy', 'AT2G04410' => 'ath', 'AT2G17660' => 'ath', 'AT3G48450' => 'ath', 'AT4G35655' => 'ath', 'AT5G40645' => 'ath', 'AT5G55850' => 'ath', 'AT5G63270' => 'ath', 'ATR0691G241' => 'atr', 'ATR0751G019' => 'atr', 'ATR0824G147' => 'atr', 'Atru.chr2.3703' => 'acertr', 'Atru.chr3.947' => 'acertr', 'Atru.chr6.2470' => 'acertr', 'Atru.chr9.998' => 'acertr', 'AUR62017121' => 'cqu', 'BcaB01g00808' => 'bca', 'BcaB02g10652' => 'bca', 'BcaB05g22232' => 'bca', 'BcaB05g23021' => 'bca', 'BcaB05g23022' => 'bca', 'BcaB05g24548' => 'bca', 'BcaB06g27541' => 'bca', 'BcaB07g29679' => 'bca', 'BcaB07g31713' => 'bca', 'BcaB07g31716' => 'bca', 'BcaB07g31717' => 'bca', 'BcaB08g34467' => 'bca', 'BcaB08g34750' => 'bca', 'BcaC01g02342' => 'bca', 'BcaC01g02573' => 'bca', 'BcaC01g02900' => 'bca', 'BcaC01g03207' => 'bca', 'BcaC01g03299' => 'bca', 'BcaC03g18191' => 'bca', 'BcaC04g20193' => 'bca', 'BcaC04g20195' => 'bca', 'BcaC04g22957' => 'bca', 'BcaC04g22958' => 'bca', 'BcaC06g36293' => 'bca', 'BcaC07g39331' => 'bca', 'BcaC08g44474' => 'bca', 'BcaC09g49861' => 'bca', 'BcaNung07006' => 'bca', 'BolC1t03140H' => 'bol', 'BolC2t07686H' => 'bol', 'BolC3t14045H' => 'bol', 'BolC3t17664H' => 'bol', 'BolC3t17761H' => 'bol', 'BolC3t18119H' => 'bol', 'BolC3t18585H' => 'bol', 'BolC3t18912H' => 'bol', 'BolC4t26349H' => 'bol', 'BolC6t37124H' => 'bol', 'BolC7t40966H' => 'bol', 'BolC7t41474H' => 'bol', 'BolC8t49975H' => 'bol', 'BolC9t54239H' => 'bol', 'BolC9t57532H' => 'bol', 'BraA02t06014Z' => 'bra', 'BraA02t09191Z' => 'bra', 'BraA03t10682Z' => 'bra', 'BraA03t13560Z' => 'bra', 'BraA04t17029Z' => 'bra', 'BraA06t25004Z' => 'bra', 'BraA06t25699Z' => 'bra', 'BraA06t26307Z' => 'bra', 'BraA07t28135Z' => 'bra', 'BraA07t29738Z' => 'bra', 'BraA09t36787Z' => 'bra', 'BraA10t43402Z' => 'bra', 'C02p15780' => 'bna', 'C03p16220' => 'bna', 'C03p54720' => 'bna', 'C03p58580' => 'bna', 'C03p63320' => 'bna', 'C03p66390' => 'bna', 'C04p47480' => 'bna', 'C06p19290' => 'bna', 'C07p05670' => 'bna', 'C07p10250' => 'bna', 'C09p13490' => 'bna', 'C09p46830' => 'bna', 'CAN.G437.16' => 'can', 'CAN.G473.46' => 'can', 'CAN.G478.16' => 'can', 'CAN.G623.18' => 'can', 'CAN.G791.5' => 'can', 'CANSAT01G0978' => 'cansat', 'CANSAT11G2601' => 'cansat', 'CANSAT64G0334' => 'cansat', 'CANSAT64G0476' => 'cansat', 'CARHR102270' => 'chi', 'CARHR107890' => 'chi', 'CARHR157210' => 'chi', 'CARHR244000' => 'chi', 'CARHR261310' => 'chi', 'CARHR269220' => 'chi', 'CARHR277120' => 'chi', 'Carub.0003s2606' => 'cru', 'Carub.0003s3176' => 'cru', 'Carub.0005s1463' => 'cru', 'Carub.0007s0464' => 'cru', 'Carub.0007s3484' => 'cru', 'Carub.0008s1620' => 'cru', 'Carub.0008s2402' => 'cru', 'Ca_05567_v3' => 'car', 'Ca_06400_v3' => 'car', 'Ca_26569_v3' => 'car', 'Cc00_g18630' => 'ccan', 'Cc05_g15040' => 'ccan', 'CDE01G0060' => 'cde', 'CDE02G4308' => 'cde', 'CDE05G1745' => 'cde', 'CDE05G3449' => 'cde', 'CDE07G0723' => 'cde', 'Cfa014215' => 'cfa', 'Cfa016909' => 'cfa', 'Ciclev10010079m.g' => 'ccl', 'Ciclev10017698m.g' => 'ccl', 'Ciclev10018013m.g' => 'ccl', 'Ciclev10027348m.g' => 'ccl', 'CiPaw.03G048700' => 'cil', 'CiPaw.03G282600' => 'cil', 'CiPaw.04G032000' => 'cil', 'CiPaw.04G197500' => 'cil', 'CiPaw.11G204700' => 'cil', 'CiPaw.12G139000' => 'cil', 'ClCG02G009120' => 'cla', 'ClCG03G003430' => 'cla', 'ClCG05G013020' => 'cla', 'ClCG05G026180' => 'cla', 'ClCG09G021410' => 'cla', 'ClCG10G004410' => 'cla', 'COL.COLO4_03570' => 'col', 'COL.COLO4_08560' => 'col', 'COL.COLO4_09847' => 'col', 'COL.COLO4_14057' => 'col', 'COL.COLO4_22527' => 'col', 'COL.COLO4_23552' => 'col', 'Cpa.g.sc130.57' => 'cpa', 'Cpa.g.sc211.36' => 'cpa', 'Cpa.g.sc4.52' => 'cpa', 'Cpa.g.sc6.329' => 'cpa', 'Cpa.g.sc959.3' => 'cpa', 'CsaV3_1G009220' => 'csa', 'CsaV3_3G004190' => 'csa', 'CsaV3_3G027510' => 'csa', 'CsaV3_5G030660' => 'csa', 'CsaV3_6G009710' => 'csa', 'CsaV3_7G011460' => 'csa', 'CSS0005019' => 'camsi', 'CSS0005705' => 'camsi', 'CSS0026643' => 'camsi', 'CSS0031996' => 'camsi', 'CSS0032386' => 'camsi', 'CSS0033103' => 'camsi', 'CSS0036176' => 'camsi', 'CSS0046177' => 'camsi', 'DCAR_011282' => 'dca', 'DCAR_012895' => 'dca', 'DCAR_017074' => 'dca', 'DCAR_019225' => 'dca', 'DCAR_021750' => 'dca', 'Dinv11115' => 'din', 'Dinv21309' => 'din', 'Dinv25706' => 'din', 'Dinv26595' => 'din', 'Dinv33395' => 'din', 'Dinv40867' => 'din', 'Duzib133G1150' => 'dzi', 'Duzib138G0703' => 'dzi', 'Duzib170G0026' => 'dzi', 'Duzib211G0666' => 'dzi', 'Duzib213G0706' => 'dzi', 'Duzib268G0900' => 'dzi', 'Duzib268G1215' => 'dzi', 'ECA234G4488' => 'eca', 'ECA236G3499' => 'eca', 'ECA238G4605' => 'eca', 'ECA240G1767' => 'eca', 'ECA240G2237' => 'eca', 'EL10Ac4g07548' => 'bvu', 'EL10Ac4g09169' => 'bvu', 'Eucgr.F03683' => 'egr', 'Eucgr.J02272' => 'egr', 'Eucgr.K02761' => 'egr', 'FAN02G0712' => 'fan', 'FAN02G0814' => 'fan', 'FAN04G0798' => 'fan', 'FAN05G0372' => 'fan', 'FAN05G3248' => 'fan', 'FAN09G2430' => 'fan', 'FAN09G3801' => 'fan', 'FAN11G1597' => 'fan', 'FAN13G2780' => 'fan', 'FAN14G3150' => 'fan', 'FAN14G3216' => 'fan', 'FAN16G1648' => 'fan', 'FAN17G1016' => 'fan', 'FAN21G4026' => 'fan', 'FAN25G0025' => 'fan', 'FvH4_3g42920' => 'fve', 'FvH4_4g24970' => 'fve', 'FvH4_5g07230' => 'fve', 'FvH4_6g40550' => 'fve', 'FvH4_6g52270' => 'fve', 'Glyma.02G301100' => 'gma', 'Glyma.02G308200' => 'gma', 'Glyma.05G044400' => 'gma', 'Glyma.08G330400' => 'gma', 'Glyma.11G245900' => 'gma', 'Glyma.14G013000' => 'gma', 'Glyma.17G126900' => 'gma', 'Glyma.17G184500' => 'gma', 'Glyma.17G193000' => 'gma', 'Glyma.17G193500' => 'gma', 'Glyma.18G011300' => 'gma', 'Glyma.18G075900' => 'gma', 'Glyma.U031319' => 'gma', 'Gohir.A01G092300' => 'ghi', 'Gohir.A02G176300' => 'ghi', 'Gohir.A03G130900' => 'ghi', 'Gohir.A04G004800' => 'ghi', 'Gohir.A09G244850' => 'ghi', 'Gohir.A11G148400' => 'ghi', 'Gohir.A11G276400' => 'ghi', 'Gohir.A12G187700' => 'ghi', 'Gohir.A13G132000' => 'ghi', 'Gohir.D01G076700' => 'ghi', 'Gohir.D02G154700' => 'ghi', 'Gohir.D03G003600' => 'ghi', 'Gohir.D05G385100' => 'ghi', 'Gohir.D09G245650' => 'ghi', 'Gohir.D11G155200' => 'ghi', 'Gohir.D11G286800' => 'ghi', 'Gohir.D12G190600' => 'ghi', 'Gohir.D13G135400' => 'ghi', 'Gorai.002G101100' => 'gra', 'Gorai.003G003800' => 'gra', 'Gorai.005G173700' => 'gra', 'Gorai.006G270200' => 'gra', 'Gorai.007G165500' => 'gra', 'Gorai.007G310200' => 'gra', 'Gorai.008G204500' => 'gra', 'Gorai.009G451800' => 'gra', 'Gorai.013G151900' => 'gra', 'GSVIVG01003976001' => 'vvi', 'GSVIVG01007562001' => 'vvi', 'GSVIVG01014701001' => 'vvi', 'GSVIVG01030113001' => 'vvi', 'HanXRQChr03g0075021' => 'han', 'HanXRQChr07g0199141' => 'han', 'HanXRQChr08g0225911' => 'han', 'HanXRQChr10g0306831' => 'han', 'HanXRQChr13g0389991' => 'han', 'HanXRQChr14g0451021' => 'han', 'Haze_09838' => 'cav', 'Haze_14795' => 'cav', 'Hma1.2p1_1287F.1_g273280' => 'hma', 'Hma1.2p1_1516F.1_g288290' => 'hma', 'HPP92_011056' => 'vpl', 'HPP92_019778' => 'vpl', 'HPP92_020592' => 'vpl', 'Hund23099' => 'sun', 'Hund29129' => 'sun', 'Hund29138' => 'sun', 'Lalb_Chr07g0183211' => 'lal', 'Lalb_Chr07g0185601' => 'lal', 'Lalb_Chr10g0107441' => 'lal', 'Lalb_Chr11g0075621' => 'lal', 'Lalb_Chr14g0362971' => 'lal', 'Lalb_Chr15g0082181' => 'lal', 'Lalb_Chr22g0360581' => 'lal', 'Lalb_Chr23g0277801' => 'lal', 'Lj4g0003884' => 'lja', 'Lj4g0020799' => 'lja', 'Lj6g0012285' => 'lja', 'Lj6g0021564' => 'lja', 'LjContig00081g0016111' => 'lja', 'Lsat_1_v5_gn_2_93560' => 'lsa', 'Lsat_1_v5_gn_5_122181' => 'lsa', 'Lsat_1_v5_gn_9_88740' => 'lsa', 'Manes.03G142000' => 'mes', 'Manes.06G114300' => 'mes', 'Manes.12G063600' => 'mes', 'Manes.13G061000' => 'mes', 'Manes.14G055632' => 'mes', 'Manes.14G055700' => 'mes', 'Manes.15G154800' => 'mes', 'Manes.17G108550' => 'mes', 'MD03G1028600' => 'mdo', 'MD06G1158600' => 'mdo', 'MD09G1019200' => 'mdo', 'MD09G1128500' => 'mdo', 'MD11G1032200' => 'mdo', 'MD13G1107600' => 'mdo', 'MD14G1165000' => 'mdo', 'MD15G1247700' => 'mdo', 'MD15G1337200' => 'mdo', 'MD17G1019800' => 'mdo', 'MD17G1117900' => 'mdo', 'Medtr3g086160' => 'mtr', 'Medtr4g104085' => 'mtr', 'Medtr5g096030' => 'mtr', 'Medtr5g098260' => 'mtr', 'Medtr8g089560' => 'mtr', 'MELO3C011903.2' => 'cme', 'MELO3C014114.2' => 'cme', 'MELO3C024949.2' => 'cme', 'MELO3C025943.2' => 'cme', 'Migut.H00042' => 'egut', 'Migut.H00949' => 'egut', 'Migut.H01752' => 'egut', 'Migut.K01429' => 'egut', 'Migut.M01646' => 'egut', 'MSTRG.3121' => 'ama', 'Nitab4.5_0000006g0630' => 'nta', 'Nitab4.5_0000622g0040' => 'nta', 'Nitab4.5_0000756g0020' => 'nta', 'Nitab4.5_0000935g0080' => 'nta', 'Nitab4.5_0001031g0240' => 'nta', 'Nitab4.5_0002404g0020' => 'nta', 'Nitab4.5_0004583g0100' => 'nta', 'Nitab4.5_0004644g0060' => 'nta', 'Nitab4.5_0006992g0080' => 'nta', 'Nitab4.5_0007779g0040' => 'nta', 'Nitab4.5_0009864g0050' => 'nta', 'Nn1g03155' => 'nnu', 'Nn1g07532' => 'nnu', 'Nn3g16602' => 'nnu', 'Oeu004788.1' => 'oeu', 'Oeu013965.1' => 'oeu', 'Oeu049408.1' => 'oeu', 'Oeu056863.1' => 'oeu', 'Oeu062395.2' => 'oeu', 'Os04g0620600' => 'osa', 'Os06g0286375' => 'osa', 'Os09g0253000' => 'osa', 'Peaxi162Scf00006g00317' => 'pax', 'Peaxi162Scf00047g02039' => 'pax', 'Peaxi162Scf00090g00142' => 'pax', 'Peaxi162Scf00139g01223' => 'pax', 'Peaxi162Scf00171g00821' => 'pax', 'Peaxi162Scf00700g00230' => 'pax', 'Peaxi162Scf00802g00032' => 'pax', 'PGR031G1012' => 'pgr', 'PGR083G0719' => 'pgr', 'PGR083G1488' => 'pgr', 'PGR083G2628' => 'pgr', 'PGR102G1484' => 'pgr', 'PGSC0003DMG400010901' => 'stu', 'PGSC0003DMG400012623' => 'stu', 'PGSC0003DMG402004292' => 'stu', 'PGSC0003DMG402017380' => 'stu', 'Phvul.001G257600' => 'pvu', 'Phvul.002G257800' => 'pvu', 'Phvul.006G058100' => 'pvu', 'Phvul.008G279500' => 'pvu', 'Phvul.008G288101' => 'pvu', 'Potri.001G338500' => 'ptr', 'Potri.001G368900' => 'ptr', 'Potri.011G094200' => 'ptr', 'Potri.012G092601' => 'ptr', 'Potri.014G168900' => 'ptr', 'Potri.015G089201' => 'ptr', 'Prupe.1G238800' => 'ppe', 'Prupe.3G196700' => 'ppe', 'Prupe.3G297800' => 'ppe', 'Prupe.5G158200' => 'ppe', 'Prupe.6G024600' => 'ppe', 'Psat2g003240' => 'psa', 'Psat4g064600' => 'psa', 'Psat5g093480' => 'psa', 'Psat5g166760' => 'psa', 'Psat7g060080' => 'psa', 'PSO063G4948' => 'pso', 'PSO478G5255' => 'pso', 'PSO541G0758' => 'pso', 'PSO675G5471' => 'pso', 'PSO782G1076' => 'pso', 'QL02p073347' => 'qlo', 'QL04p067770' => 'qlo', 'QL04p067789' => 'qlo', 'QL08p003901' => 'qlo', 'QL10p005494' => 'qlo', 'RcHm_v2.0_Chr2g0155811' => 'rch', 'RcHm_v2.0_Chr5g0076961' => 'rch', 'RcHm_v2.0_Chr6g0295941' => 'rch', 'RcHm_v2.0_Chr7g0191421' => 'rch', 'Rhsim04G0012000' => 'rsi', 'Rhsim06G0142700' => 'rsi', 'Rhsim06G0143100' => 'rsi', 'Rhsim06G0177500' => 'rsi', 'Rhsim06G0230600' => 'rsi', 'Rhsim08G0046900' => 'rsi', 'Rhsim08G0183500' => 'rsi', 'Rhsim12G0171500' => 'rsi', 'RhsimUnG0150800' => 'rsi', 'Sabra12G0067300' => 'sbr', 'Sabra14G0128800' => 'sbr', 'Sabra16G0219200' => 'sbr', 'Sabra16G0241800' => 'sbr', 'SalBow1G1481' => 'sbo', 'SalBow7G4786' => 'sbo', 'SalBow8G0601' => 'sbo', 'SalBow8G5236' => 'sbo', 'Sc03g0011490' => 'sci', 'Sc16g0003740' => 'sci', 'Sc16g0008160' => 'sci', 'Sc20g0004010' => 'sci', 'Sc22g0002110' => 'sci', 'Sed0001295' => 'sed', 'Sed0002224' => 'sed', 'Sed0003830' => 'sed', 'Sed0005274' => 'sed', 'Sed0006284' => 'sed', 'Sed0007937' => 'sed', 'Sed0020982' => 'sed', 'Sed0023922' => 'sed', 'Sed0025558' => 'sed', 'Sed0028000' => 'sed', 'SGA_v2.0_scaffold42G15979' => 'sas', 'SMO143G0047' => 'smo', 'SMO356G0317' => 'smo', 'SMO367G0516' => 'smo', 'Solyc02g093670.3' => 'sly', 'Solyc07g045340.4' => 'sly', 'Solyc07g065640.3' => 'sly', 'Solyc12g006080.2' => 'sly', 'Sopen02g038300' => 'spe', 'Sopen07g023880' => 'spe', 'Sopen07g033850' => 'spe', 'Sopen12g002040' => 'spe', 'Sp2g26390' => 'spa', 'Sp3g23220' => 'spa', 'Sp3g31000' => 'spa', 'Sp5g13580' => 'spa', 'Sp6g17730' => 'spa', 'Sp7g01220' => 'spa', 'Sp7g33430' => 'spa', 'TAR374G0070' => 'tar', 'TAR622G0708' => 'tar', 'TAR629G0801' => 'tar', 'TAR629G1288' => 'tar', 'THA.LOC104798957' => 'tha', 'THA.LOC104802627' => 'tha', 'THA.LOC104807436' => 'tha', 'THA.LOC104808840' => 'tha', 'THA.LOC104813450' => 'tha', 'THA.LOC104817708' => 'tha', 'THA.LOC104819034' => 'tha', 'THA.LOC104821502' => 'tha', 'THA.LOC104822437' => 'tha', 'THA.LOC104826632' => 'tha', 'THA.LOC109116874' => 'tha', 'Thecc.01G008100' => 'tca', 'Thecc.01G197300' => 'tca', 'Thecc.01G197900' => 'tca', 'Thecc.02G269200' => 'tca', 'Thecc.03G121500' => 'tca', 'Thecc.07G011600' => 'tca', 'Thhalv10002884m.g' => 'esa', 'Thhalv10005223m.g' => 'esa', 'Thhalv10011071m.g' => 'esa', 'Thhalv10015980m.g' => 'esa', 'Thhalv10023043m.g' => 'esa', 'Thhalv10026942m.g' => 'esa', 'Thhalv10028011m.g' => 'esa', 'TPR.G14238' => 'tpr', 'TPR.G15060' => 'tpr', 'TPR.G24138' => 'tpr', 'TPR.G24141' => 'tpr', 'TPR.G37471' => 'tpr', 'TPR.G6187' => 'tpr', 'TPR.G8588' => 'tpr', 'TWI14G0058' => 'twi', 'TWI18G0320' => 'twi', 'TWI38G1088' => 'twi', 'TWI38G1627' => 'twi', 'TWI39G0644' => 'twi', 'unitig_0.g1594' => 'ugi', 'unitig_1.g29341' => 'ugi', 'unitig_747.g21637' => 'ugi', 'vmacro09640' => 'vma', 'vmacro11598' => 'vma', 'vmacro12072' => 'vma', 'vmacro16701' => 'vma', 'VMungo0540G2058' => 'vmu', 'Zm00001eb070350' => 'zma', 'Zm00001eb189200' => 'zma', 'Zm00001eb280910' => 'zma', 'Zm00001eb380850' => 'zma' ) $gf_id = 'HOM05D001153' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001153' ) $data_identifier = 'HOM05D001153' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 28, 'bol' => (int) 15, 'bra' => (int) 12, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 6, 'cpa' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 13, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mdo' => (int) 11, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 10, 'sas' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 11, 'tca' => (int) 6, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 1, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380850' $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